CCM, so happy to hear of your daughter’s progress. I am still a fan of the WAPF diet. I think a lot of people here are, although a lot of people, like you, don’t soak and sourdough grains at home. I am not strict WAPF at all, and eat some refined grains like pasta, etc., but mostly eat whole foods and go for raw dairy when possible. I think the diet has gotten a bad rap here because a lot of WAPF followers have gone low-carb with it.
I would not be surprised if your daughter benefited from refusing meds. I am of the opinion that most help reduce symptoms short-term but create some worse long-term issues, and as you note, can absolutely suppress healing. I hope her experience can give others guidance.